How protein molecules “rock” in crystals: SPbU scientists

The group of scientists from St Petersburg University headed by the Director of the Laboratory of Biomolecular NMR Nikolai Skrynnikov discovered how protein molecules rock in crystals.

X-ray crystallography is a technique used for decoding the protein structure — but it generally requires a pure crystal of high regularity. A crystal is, as we can presume, something solid and stable in shape. Yet the protein molecules can rock in crystals, the scientists discovered. Although the amplitude is slight, it is enough to distort the results of the X-ray diffraction and two-dimensional NMR spectroscopy. What is important is to solve the structure of a complicated arrangement of atoms in the proteins. Today at the core of the molecular biology are our results of the X-ray crystallography. In particular, the recent advances in the X-ray crystallography make it possible to develop new drugs.

SPbU scientists and Paul Schanda from the Structural Biology Institute in Grenoble carried out an experiment that allowed to get a complete picture of the temporal characteristics of the ‘rocking’ motion of the protein molecules. In the ubiquitin, it is tens of microseconds.

Moreover, the scientists successfully defined dynamics of local conformation in different crystal forms, in particular flips in the β-turn regions. “The data we obtained by modelling by a method of molecular dynamics show that the peptide bonds that form the crystal lattice can considerably influence this motion, — said Nikolai Skrynnikov. — As a result, we assume that the overall motion is to some extent coupled to local dynamics. However we need to continue our series of experiment to prove it”.

In future, this methodology can make protein crystallization more effective: for example, we can use point mutations to modify the crystal bonds to decrease the amplitude of the ‘rocking’ motion and therefore increase the quality of the X-ray data, say SPbU scientists.

SPbU post-graduate student Sergei Izmailov and Candidate of Sciences Olga Rogacheva from the Department of Biochemistry have significantly benefit the project. The fact that we obtain these results is due to factors: first, talented and committed young scientists and financial support from the Russian Science Foundation, says Nikolai Skrynnikov. The study is published in Nature Communications.